Rice dwarf virus (RDV), a member of phytoreovirus genus, is a double-shelled dsRNA virus infecting rice crops. In contrast to its detailed biochemical characterization due to the severe economical consequence of rice infection in Asia, structural information on RDV is scarce and controversial. We have determined the three-dimensional structures of the full (with dsRNA) and empty RDV (no RNA) particles at 25 resolution by 400 kV electron cryomicroscopy and computer reconstruction. Rice dwarf virus (RDV), a member of the Reoviridae family, is a dsRNA virus. Infection of rice plants reduces crop production significantly. The three-dimensional structure of the 700 wide RDV capsid determined by 400 kV electron cryomicroscopy and computer reconstruction reveals two distinctive icosahedral shells: an outer shell having a T=13 icosahedral lattice composed of 260 trimeric clusters and an inner T=1 icosahedral lattice of 60 dimers. This symmetry mismatch is accommodated by structural variations in the floor domains of the outer shell proteins in the quasi-equivalent subunits. The calculated masses of the putative monomeric subunits are consistent with an assignment of the 46 kDa P8 and the 114 kDa P3 to the major outer and inner shell proteins respectively. The primary and three-dimensional structure of P8 are compared with those of VP7 of blue-tongue virus (BTV), an animal reovirus. Though their overall sequence homology shows 28% identity, the mass densities in the upper domain of P8 matches well with the beta sandwich domain seen in the crystal structure of VP7. The lower domain of P8 fits but less well to the alpha helical domain of VP7 even after allowing for twisting between the two domains. The structural variations seen P8 suggests a breakdown of the quasi-equivalence rule, though VP7 follows it strictly.